PDB-4gxh: Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (targe...

ID or keywords:

Entry

Database: PDB / ID: 4gxh

Title

Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from Xenorhabdus bovienii SS-2004

Components

Pyrrolidone-carboxylate peptidase

Keywords

HYDROLASE /

Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium

Function / homology

Function and homology information

pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity /

proteolysis /

cytosol
Similarity search - Function

Biological species

Xenorhabdus bovienii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.7 Å

Authors

Ghosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: To be Published
Title: Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from Xenorhabdus bovienii SS-2004 (CASP Target)
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium

History

Deposition	Sep 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gxh.cif.gz	320.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4gxh.ent.gz	264.1 KB	Display	PDB format
PDBx/mmJSON format	4gxh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gx/4gxh ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gxh	HTTPS FTP

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Related structure data

Similar structure data	3ro0-d 3rnz-d 3lac-2 5z47-1 5cqg-2 1aug-d 1pnv-d 3m7v-d 6ltq-d 6jom-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-012831

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyrrolidone-carboxylate peptidase

B: Pyrrolidone-carboxylate peptidase

C: Pyrrolidone-carboxylate peptidase

D: Pyrrolidone-carboxylate peptidase

hetero molecules

94.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	117.179, 117.179, 186.615
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22

Details

There is 1 biological unit (a tetramer) in the asymmetric unit (chain A, B, C, D)

#1: Protein	Pyrrolidone-carboxylate peptidase / 5-oxoprolyl-peptidase / Pyroglutamyl-peptidase I Mass: 23365.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenorhabdus bovienii (bacteria) / Strain: SS-2004 / Gene: pcp, XBJ1_1667 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL / References: UniProt: D3V0W1, pyroglutamyl-peptidase I
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.43 Å³/Da / Density % sol: 64.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M Na2HPO4/KH2PO4, 2.5 M Sodium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 77 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2012

Radiation

Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 2.7→50 Å / Num. all: 68317 / Num. obs: 40725 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / B_iso Wilson estimate: 59.83 Å² / R_merge(I) obs: 0.091 / R_sym value: 0.063 / Χ²: 1.227 / Net I/σ(I): 14.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.7-2.75	5.3	0.89	3433	1.531	1	100
2.75-2.8	5.3	0.708	3395	1.506	1	100
2.8-2.85	5.3	0.625	3432	1.469	1	100
2.85-2.91	5.3	0.537	3435	1.454	1	100
2.91-2.97	5.3	0.409	3395	1.4	1	100
2.97-3.04	5.3	0.329	3400	1.394	1	100
3.04-3.12	5.3	0.272	3426	1.326	1	100
3.12-3.2	5.3	0.234	3405	1.327	1	100
3.2-3.3	5.3	0.186	3429	1.278	1	100
3.3-3.4	5.4	0.138	3415	1.187	1	100
3.4-3.52	5.3	0.115	3430	1.17	1	100
3.52-3.66	5.4	0.102	3432	1.117	1	100
3.66-3.83	5.3	0.088	3368	1.068	1	100
3.83-4.03	5.3	0.083	3451	1.069	1	100
4.03-4.29	5.3	0.075	3393	1.012	1	99.9
4.29-4.62	5.3	0.071	3406	1.088	1	99.6
4.62-5.08	5.3	0.066	3427	1.001	1	99.9
5.08-5.81	5.2	0.056	3417	1.018	1	100
5.81-7.32	5.2	0.05	3431	1.067	1	99.9
7.32-50	5.4	0.037	3397	1.066	1	99.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
MOLREP		phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
CBASS		data collection
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: A low resolution de-novo phased structure

Resolution: 2.7→45.691 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
Details: THERE ARE UNMODELED DENSITIES NEAR CYS143 (PUTATIVE NUCLEOPHILE) SIDE CHAINS IN ALL PROTOMERS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	1821	5.01 %	RANDOM
R_work	0.176	-	-	-
obs	0.1782	36353	99.77 %	-
all	-	40725	-	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 206.47 Å² / B_iso mean: 47.7633 Å² / B_iso min: 11.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→45.691 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6154	0	29	96	6279

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6338
X-RAY DIFFRACTION	f_angle_d	1.383	8669
X-RAY DIFFRACTION	f_chiral_restr	0.081	1016
X-RAY DIFFRACTION	f_plane_restr	0.007	1125
X-RAY DIFFRACTION	f_dihedral_angle_d	14.908	2278

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.7001-2.7731	0.2907	136	0.2443	2598	2734	100
2.7731-2.8547	0.2816	131	0.2586	2631	2762	100
2.8547-2.9468	0.3236	143	0.2484	2599	2742	100
2.9468-3.0521	0.2727	112	0.2351	2632	2744	100
3.0521-3.1742	0.3076	143	0.2246	2623	2766	100
3.1742-3.3187	0.2717	142	0.2147	2636	2778	100
3.3187-3.4936	0.2279	151	0.1947	2615	2766	100
3.4936-3.7124	0.2152	130	0.1813	2637	2767	100
3.7124-3.9989	0.2254	150	0.1628	2656	2806	100
3.9989-4.401	0.197	133	0.1402	2658	2791	100
4.401-5.0371	0.1638	152	0.1289	2671	2823	100
5.0371-6.3435	0.186	143	0.1601	2724	2867	100
6.3435-45.6976	0.2003	155	0.1678	2852	3007	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.4289	-0.1698	0.1648	3.3323	0.5346	3.6262	-0.1523	-1.1539	-0.7006	0.1558	0.1865	-0.7353	0.8537	-0.3416	0.1118	0.5971	0.2201	0.0223	0.4606	0.0376	0.7301	-37.649	-2.5806	8.6369
2	1.3374	-0.5815	-0.739	1.7129	0.2627	0.6923	-0.3104	0.3505	-0.6575	-0.4272	-0.0881	-0.1521	0.7495	0.1948	-0.0393	0.8034	0.0917	0.2219	0.2202	-0.1543	0.5964	-40.2137	-1.097	2.659
3	2.0096	-0.028	0.0949	3.2617	-3.1435	4.5891	-0.4887	-0.6856	-0.5445	-0.176	0.2538	-0.5037	0.2962	-0.3858	0.145	0.5022	0.2381	0.1466	0.5514	0.0944	0.7619	-21.2549	4.7918	7.23
4	0.3651	-0.3178	0.2089	1.0132	-0.9385	0.9038	-0.3678	0.3392	-0.2613	-0.5681	0.0754	-0.0876	0.2717	0.031	0.0656	0.5699	0.0941	0.0812	0.3406	-0.1083	0.396	-37.1133	9.2434	-1.336
5	1.2677	-0.0464	-1.2268	3.1759	0.9577	2.073	-0.0905	-0.0944	-0.2566	-0.0771	0.1586	0.0344	-0.4832	-0.115	0.106	0.4191	0.0945	0.0009	0.2309	-0.0043	0.4461	-40.0445	6.8931	11.9235
6	2.9043	-0.611	0.6925	2.2376	-0.4844	5.5186	0.2105	0.0591	-0.5089	-0.3548	0.0971	0.6485	0.3799	0.2107	0.0192	0.4118	0.0217	-0.026	0.217	-0.1477	0.578	-51.1934	4.3187	5.449
7	5.0588	-0.4818	-0.4411	5.1617	1.2134	7.0729	-0.116	0.3439	-0.217	-0.2824	-0.1712	0.4604	-0.3854	-0.815	0.2944	0.2247	0.0615	0.0537	0.3252	-0.0259	0.446	-62.2033	14.5225	32.6402
8	2.2897	0.3762	-0.7533	2.4217	0.7927	1.9163	-0.0467	-0.3228	0.2733	0.188	-0.1433	0.3245	0.0353	-0.2058	0.1663	0.2464	0.0691	0.0394	0.3818	-0.0395	0.3382	-53.8059	23.5553	38.2221
9	2.4447	-0.101	-0.889	1.234	1.3932	2.4882	0.0194	0.0096	0.1895	-0.1975	-0.0417	-0.0324	0.1283	0.577	-0.1327	0.2456	0.0657	0.026	0.2997	-0.015	0.3652	-51.5845	18.1477	27.3877
10	5.0479	-0.0912	-0.5365	5.7507	0.5823	8.9836	-0.4335	-0.45	-0.4607	-0.0529	-0.2652	-0.0352	0.3519	-0.2221	0.258	0.3041	0.0208	0.0739	0.2291	0.0344	0.4453	-53.7426	7.1007	35.1502
11	4.2897	0.9775	-0.6296	1.7706	-1.2151	5.3483	-0.1809	-0.6269	0.3105	0.1115	0.0811	-0.3666	0.1974	0.7927	0.1364	0.3562	-0.0349	-0.1296	0.5415	-0.0894	0.3927	-19.4825	37.9797	37.7239
12	2.4324	-0.2377	0.7495	0.9859	-0.1561	1.5565	0.0977	-0.861	0.219	0.3557	0.1052	-0.1613	-0.0974	0.5665	-0.1883	0.3521	-0.0365	-0.0779	0.6573	-0.0955	0.4111	-25.6276	34.9623	43.1734
13	1.7687	-0.0972	0.8631	5.3491	0.5246	1.7252	-0.1367	-0.2847	-0.1725	0.1004	-0.0169	-0.4228	0.0392	-0.0575	0.3171	0.4222	0.148	-0.0681	0.7846	0.2055	0.3811	-29.4625	17.9409	44.6512
14	1.5418	0.2593	-0.4426	0.9613	-0.5312	1.2208	0.2246	-0.6872	0.2063	0.1656	-0.1315	0.3216	-0.1645	0.3258	-0.0818	0.3118	0.0461	-0.0101	0.522	-0.0835	0.3192	-35.2602	35.1576	40.8103
15	4.3387	-0.803	-3.1325	3.5894	3.7988	8.7306	-0.1778	-0.2244	-0.1139	-0.0026	-0.1693	-0.1669	0.0937	0.2118	0.2048	0.1784	0.0498	-0.0876	0.4283	0.0407	0.2607	-26.5879	32.0053	31.4004
16	3.0596	-1.9065	-2.3638	5.3055	3.7323	3.0741	0.1152	-0.4634	1.2638	0.3418	0.2073	-0.9838	-0.4421	0.6993	-0.1669	0.384	-0.0436	-0.0744	0.3659	-0	0.4857	-25.6556	44.536	31.4136
17	7.5201	-0.4632	-0.2947	4.5161	0.6805	5.3274	0.3542	0.1816	0.1605	-0.4757	-0.3601	-0.2756	-0.5268	-0.0261	0.1815	0.4129	-0.0378	0.0607	0.4025	0.1427	0.3578	-20.0854	39.0964	1.7458
18	1.1257	0.599	0.2109	2.1169	-0.4032	1.8945	-0.229	0.3869	0.0069	-0.8131	0.251	-0.3525	-0.092	0.0255	-0.0286	0.5743	-0.0062	0.1173	0.3767	0.0604	0.311	-23.0956	32.8473	-3.6871
19	1.7684	-1.0269	-0.6562	7.4332	2.6109	1.0897	-0.3526	0.1143	0.4884	-0.3652	0.1849	0.0947	-0.3096	-0.1944	0.2416	0.6907	0.1195	-0.1561	0.4403	0.0319	0.4034	-40.1399	29.0897	-5.2883
20	1.3298	0.3785	0.266	1.9879	0.0876	2.0402	-0.139	0.2643	-0.4308	-0.6796	0.1379	-0.3406	0.0132	0.3609	0.0904	0.5297	0.0674	0.1059	0.3831	0.0404	0.374	-22.1037	23.7572	-2.09
21	8.7034	-2.6635	-2.2002	2.4685	2.3051	2.7018	-0.7424	0.1579	-0.1449	0.5637	0.1425	0.0718	0.1133	-0.4352	0.3998	0.3588	0.0541	-0.0076	0.3087	0.0341	0.3267	-31.9172	35.7063	16.107
22	5.5125	-0.7537	-1.9874	5.0376	1.2433	9.0065	0.2227	0.0432	0.0059	-0.6087	0.0053	-0.9856	-0.4226	0.9613	-0.0874	0.2159	-0.011	0.0384	0.3217	0.0349	0.4658	-12.7108	31.5739	6.7664

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 18 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 84 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 104 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 105 through 157 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 158 through 185 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 186 through 203 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 34 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 35 through 157 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 158 through 185 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 186 through 205 )	B
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 35 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 36 through 84 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 85 through 104 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 105 through 157 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 158 through 185 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 186 through 203 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 35 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 36 through 84 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 85 through 104 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 105 through 168 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 169 through 185 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 186 through 206 )	D

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